ZA200604550B - Biomarkers of resistance to hiv-infections in humans and biological applications thereof - Google Patents

Abstract

The invention relates to the use of IL-22 alone or in combination as biomarker of resistance to infections in humans when added to of one or several agonists of the formyl peptide receptors (FPR) receptors family and formyl peptide receptors-like 1 (FPRL 1). Said biomarker is useful in diagnostics, prophylaxis and therapeutics.

Description

“Biomarkers of resistance to HIV-infections in humans and biological applications thereof”

The invention concerns biomarkers of resistance to infections in humans and biological applications thereof, particularly in diagnostics, prophylaxis and therapeutics.

It relates to biomarkers of resistance to infections due to pathogens in general, particularly infections due to virus and retrovirus, and more particularly to HI'V-infections.

Several viral diseases emerged at the end of the twentieth century, particularly the

Acquired Immunodeficiency Syndrome (AIDS) caused by the human immunodeficiency virus (HIV). More than two decades since its discovery, human immunodeficiency virus (HIV) epidemic is still a major burden for health, social and economical reasons on all over the world.

During 2002, about 3.1 millions of deaths were listed, while about 5 millions of new infection cases were registered. Over 40 million people are infected worldwide and there is an urgent need to find agents to prevent the spread of this virus as well as to improve on the current treatment regimen. To date, both host genetic repertoire, innate and acquired immune responses, viral mutation or attenuation have been invoked to explain the higher or lower individual susceptibility to the infection. A great deal of progress has been made in understanding the mechanism of human immunodeficiency virus entry into target cells. Landmark discoveries such as the identification of viral coreceptors and the structure of the viral envelope protein (Env) bound to its receptor provided important insight into how Env mediates fusion of the viral and cellular membranes as described in Fig. 1.

The existence of some people somewhat "immune" from infection, despite dealing with repeated HIV exposure, as well as the extremely slow disease progression in some HIV infected individuals, offers valuable clues to elucidate mechanisms underlying natural HIV resistance. Strikingly, both such cohorts, the so-called Exposed Seronegative, Exposed

Uninfected (ESN, EU) and the Slow Progressors, Long Term Progressors (SP, LTNP) individuals have common immune responses, e.g. the generation of neutralising antibodies directed against common targets, which can play a protective role in virus entry and/or spread.

In 1989 a paper by Ranki described a curious phenomenon: HIV-specific T-cell response to HIV, native gp 120 and recombinant envelope and core proteins could be detected in antibody- and antigen-negative sexual partners of known HIV-positive men [1]. Two other q reports confirmed that initial observation, and the authors raised the possibility that exposure to

HIV that did not result in seroconversion and infection would be associated with the exclusive priming of T helper lymphocytes (2, 3]. Analyses performed in different cohorts of individuals at high risk of HIV infection, and including health care workers parenterally exposed to HIV and healthy newborns of HiV-infected mothers, revealed that HIV-specific T helper cells, but not antibodies, were present in all these subjects[4]. These observations led to the hypothesis that viral exposure resulting in the exclusive priming of HIV-specific T cells could be associated with protection against actual HIV infection. This hypothesis was greatly strengthened by three commercial sex workers in Narobi [5] (the Pumwaani cohort), clearly demonstrated that whereas the majority of women who started to prostitute themselves became HIV infected within a year, a sizable minority, subsequently estimated to be around 15% of the individuals tested, was clearly resistant to infection. 2) Sarah Rowland-Jones [6] showed the presence of HIV-specific CTL in healthy newborns of HIV infected mothers. The detection of H1V-specific, IFNa- secreting CD8

T lymphocytes in these newborns was a turning point in the realization that HIV exposure not associated with seroconversion is associated with an actual abortive infection and that live, replicating virus is indeed responsible for the stimulation of specific immunity. In fact, only actual infection with the virus would result in presentation of viral antigens in association with

HLA class | molecules, and elicitation of a CD8-mediated immune response. (much later, the protective role of cell mediated immunity in this setting was further reinforced by the observation that late seroconversion occurring in Kenyan HIV-resistant sex workers who interrupt commercial sex work for a period of time is related to the waning of HIV-specific CD8+ responses due to reduced antigenic exposure)[7]. 3) Experiments in which macaques exposed in vivo to subinfectious doses of SIV, and in whom SlIV-specific T helper cells were detected, demonstrated protection against subsequent challenges with infectious doses of the same virus [8] (these result were not unequivocally confirmed by other investigators).

The field of investigation of immune correlates of protection against HIV infection was born. Subsequent, pivotal reports showed that in HIV-exposed but uninfected individuals: 1) a particular genetic background, epitomized by the .32 deletion in the CCRS receptor [9], could be present [10-12]; 2) the production of soluble factors, including cell antiviral factors (CAF) [13, 14), beta chemokines, and alpha defensins [15], is increased [16-18]; 3) secretory HIV-specific

IgA as well as T helper and CTL can be detected in cervico-vaginal fluids and ejaculates[19-22];

and 4) NK cell activity is particularly potent [23]. Thus, 15 years after the first description of the detection of HIV-specific T helper cells in seronegative individuals, possible resistance to HIV infection can be summarized as being correlated with the elicitation of systemic and mucosal cell mediated immunity, and mucosally-confined IgA, possibly within favourable genetic and natural

S immunity settings.

Table 1. Mechanisms suggested to be associated with resistance to HIV infection.

Acquired mechanisms Genetic mechanisms Innate Immunity

THIV-specific Thelpercells Deletion in the HIV-1 Elevated NK activity

Coreceptors

HIV-specific CTL Particular HLA alleles Elevated production : of B chemokines

Mucosal HI1V-specific IgA Elevated production of CAF

Anti CD4 antibodies Elevated concentration of a defensins

Anti CCRS antibodies -—

The comprehension of mechanisms of natural resistance to HIV infection may have implications for the identification of anti-viral novel strategies and in particular for the development of innovative diagnostics, therapeutics and vaccine design.

The inventors have compared studies on protein profiles (proteom) and genome expression (transcriptome) from HIV exposed uninfected individuals (EU), HIV exposed and infeceted individuals (HIV+) and healthy donnors (HC) to identify biomarkers from EU that could explain resistance mechanisms to the HIV infection.

They have identified a key cytokine which appears to be responsible for the induction of proteins involved in viral resistance.

They have also found that another cytokine shows a polymorphism among the studied cohorts exhibiting a particular pattern in EU. Then other isoforms also appear to be involved in HIV resistance processes by their effect on FPR or FPRLI receptors and the subsequent phosphorylation of CCR5 or CXCR4 HIV-co-receptors. Then the combination of these cytokines was considered as element participating indirectly to the viral infection blockade.

Individually and in combination, they also appear to participate in the HIV resistance mechanisms. [t is then an object of the invention to provide biomarkers of resistance to HIV- infections comprising such cytokines and protein of the induced cascades.

According to another object, the invention aims to provide new tools useful in diagnostics, prophylaxis and therapeutics comprising the use individually or in combination, of said cytokines and the proteins of the cascades they induce.

The invention thus relates to the use as biomarkers of the resistance to HIV infection in human of one or several agonists of the formyl peptide receptors (FPR) receptors family and formyl peptide receptors-like | (FPRL1). More particularly, said agonists are selected in the group comprising soluble SAA, WKYMWVm peptide, the bacterial chemotactic peptide fMLF and a fragment thereof of about 8.6 kDa.

The invention more specifically relates to the use as biomarkers of the resistance to

VIH infection of at least one protein of an innate immune response including 11-22, the

Jack/STAT pathway, SOCS3, beta defensines (2 and 3) and the acute phase apolipoprotein serum amyloid Ac or A-SAA or a fragment thereof, IL-8 cytokine and isoforms thereof.

Advantageously, the biomarkers are selected in the group comprising 1L-22 and/or

SOCS1 and/or STAT3 and/or a soluble protein of about 8.6 kDa as identified in plasmas by

SELDI-TOF and /or IL-8, and isoforms thereof.

The invention also relates to the use of phosphorylated STAT and/or SOCS proteins.

Alternatively and/or additionally, the invention relates to the use as biomarkers of chemokines selected in the group comprising GRO-a, MIP-3B, SDFI1-$, and the gamma chemokine lymphotactin and isoforms thereof.

Said proteins are of great value in biological applications in view of their properties as biomarkers of resistance to HIV infections. Particularly, they are of great interest in diagnostics, therapeutics and prophylaxis.

The invention thus also relates to their use as diagnostic tools comprising using said proteins. \

The invention also relates to pharmaceutical compositions for preventing or treating any infection due to pathogens, particularly viral or retro-viral infections, particularly more HIV- infections.

Such compositions comprise an effective amount of at least one of the above 5 proteins defined as biomarkers, in association with a pharmaceutically acceptable carrier.

Preferred pharmaceutical compositions comprise an effective amount of one or several proteins of the cascade comprising 11-22, Jack/STAT pathway, SOCS3, beta defensines (2 and 3) and the acute phase apolipoprotein serum amyloid Ac or A-SAA or a fragment thereof,

IL-8 cytokine and isoforms, in association with a pharmaceutically inert vehicle.

The pharmaceutical compositions of the invention are advantageously prepared for administration by the oral , intramuscular, intravenous or mucosal route.

For oral administration, they are presented in the form of tablets, pills, capsules, drops, patch or spray.

For administration by injection, the pharmaceutical compositions are under the form of solution for injection by the intravenous, subcutaneous or intramuscular route produced from sterile or sterilisable solution, or suspension or emulsion.

For administration by mucosal route, the pharmaceutical compositions are under the form of gels.

The administration doses will easily be adjusted by the one skilled in the art depending on the patient’s condition.

According to still another aspect, the invention relates to a method for favouring the innate host resistance to viral infections, comprising using at least one of the proteins above defined as biomarkers particularly 1L-22 as starter cytokine helping the innate immune response to infections.

Other characteristics and advantages of the invention will be given in the following examples and with reference to figures | to 10, which represent, respectively: = Figure | : Different steps of the viral envelop attachment to cell receptors, * Figure 2: SELDI-TOF protein profile from individuals from different cohorts, = Figure 3: Inhibitory effects on HIV-1 infection of the cascade infection EU, » Figure 4: Depletion of the protein of about 8.6 kDa using an anti-A-SAA Mab,

= Figures 5 and 6: Comparative IL-8 (Figure 5) and IL-22 (Figure 6) RT-PCR from individuals from different cohorts, * Figure 7: Western validate of SAGE analysis from individuals from different cohorts, * Figure 8: Induction of VIH-1 CCRS5 co-receptor phosphorylation by the binding acute phase SAA protein to the FPR receptor, * Figure 9: HIV-1 RS infectivity of immature dendritic cells, = Figure 10: SELDI-TOF profile of SAA preparation exhibiting the ~ 8.6 kDa fragment.

Materials and Methods

Exposed uninfected (EU) individuals recruitment

HIV exposed but uninfected individuals were enrolled in the study. In each case the ESN was the sexual partner of a HIV infected patient; in each couple a prolonged history of penetrative sexual intercourse without condom (and no other known risk factors) was reported. Inclusion criteria for the EU was a history of multiple unprotected sexual episodes for at least four years with at least four episodes of at-risk intercourse within 4 months prior to the study period. EUs were repeatedly HIV seronegative by culture and RNA virus load methods. HIV-infected individuals and healthy controls were also enrolled in the study. HIV patients and HC were age-and-sex- matched with the EU. All EU, HIV+ and HC individuals had been longitudinally followed for at least 4 years (prior to the study period) by the Department of Infectious Diseases, Santa Maria

Annunziata Hospital in Florence. This allowed us to exclude from the study ESN and HC in whom sexually transmitted diseases or any other pathology had been reported in that time period.

The EU were characterized on the basis of the presence of CCR5-A32 alleles; a heterozygous deletion was detected in 1 individual. All EU, HIV patients and low-risk uninfected individuals agreed to donate peripheral blood mononuclear cells.

Cells

Proteomic and Transcriptomic comparative studies were carried out on T cells from

EU and HIV+ forming discordant couples having frequent unprotected sexual intercourse or invasive drug injection by syringe exchanges. T cells from HC were the controls of these analyses. Peripheral blood mononuclear cells (PBMC), obtained from the 3 cohorts: HC, EU and

Hiv+ were collected and separated over Ficoll-Hypaque, were short-term (6 days) cultivated (Yssel, H. and Spits, H, in Current Protocols in Immunology, Chapter 7.19) then T lymphocytes (CD4+ and CD8+) were CD3/CD28 activated and cultivated in RPMI supplemented of 10% of

FCS. Briefly, to activate the CD3-TCR complex, 10 pg/mL of anti-CD3, SPV-T3b monoclonal antibody (MAb) was used to coat 24-well plates for 4 hr at 37°C. Subsequently, 106 cells were then deposited in these coated wells in the presence of culture medium (Yssel’s medium, Irvine scientific, Santa Ana, CA) containing 1% of AB+ human serum and 1 pg/mL of anti-CD28 L293

MAb. Three T cells activation times were respectively done 2, 6 and 18 hr. Activated cells pooled from S individuals per cohort (having each an equivalent number of cells and total RNA, Table 2) for T cell gene expression studies that were carried out using the Serial Analysis Gene

Expression (SAGE, Velculescu 1995, [24]). Subsequently, a set of total ARN of each individual of the pool was freeze for further use to validate individually the SAGE results. A set of these cells was also used to perform Power and Western blotting analyses (see below). Soluble proteins presents in the plasma of individuals (n=25, Table 2) from 3 cohorts were analysed by SELDI-

TOF Ciphergen™ approach.

Dendritic cell were derived of monocytes from healthy donors. Briefly, a buffy coat was processed to obtain highly purified monocytes that were cultivated in DMEM medium supplemented of 10% of FCS in the presence of 10 ng/mL of IL-4 and 150 ng of GM-CSF (Becton and Dickinson) for 7 days up to obtain well characterized using appropriated MAbs (anti-DC sign, Anti-CD!a, anti-CD83 and anti-CD86 MAbs) also exhibiting the presence of the

Formy) peptide receptor-like | (FPRLI) (a receptor belonging to the Formyl Peptide receptor (FPR) family) immature Dendritic Cells (iDC). Cells were maintained at 37°C in a 5% CO2 humid atmosphere.

Antibodies and Reagents

Recombinant human [L-22, anti-CCRS polyclonal Ab, anti-human 1L-22 polyclonal were purchased from R & D Systems (Oxon, UK), Serum amyloid A (A-SAA) and IL-8 proteins were purchased from Peprotech (Rocky Hill, NJ), MIP-13 was obtained from (Frangoise Baleux (Pasteur Institute, Paris, France), Anti-IL-8 MAb was purchased from Bender, Anti-CXCR4,

Anti-SAAl and 2 MAb (Biosource), Anti-SAA MAb (Calbiochem), Anti-active Stat-1 polyclonal Ab, anti- Statl MAb, Anti-active Stat-3 polycional Ab, Anti-Stat-3 pAb, anti-active

Stat-5 polyclonal Ab, Anti-Stat-5 MAb was purchased from Becton and Dickinson (Palo Alto,

CA). The anti-SOCS 3 polyclonal Ab (Santa Cruz laboratories, Santa Cruz, CA)

Plasma analysis by Protein-Chip SELDI-TOF approach

Before analyze, plasma samples were centrifuged at 13 000 rpm during 15 min, the pellet was discarded and supernatant was diluted (1:10) in optimized binding buffer (BB: NaCl 0.250 M Hepes 50 mM, pH 7.5). Diluted plasma samples were applied during 1 hr onto previous saturated strong anion exchanger (SAX2) Protein-chips™ by two BB baths of 5 min. Unbound proteins were washed out using successively 3 washes of 5 min with the washing buffer (WB:

NaCl IM, Hepes 50 mM, pH 7.5) and a final wash using 5 uL of pure bi-distilled water. The

Chip-captured proteins were subsequently air-dried at room temperature (RT) before their covering with a matrix (3,5-dimethoxy-4-hydroxycinnapynic acide (SPA) in 99.9% acetonitril and 0.1% trifluoroacetic acid) to absorb the laser energy. The matrix-prepared samples were dried at RT. These samples then received an average of 100 real time laser shots to desorb the captured proteins at a laser intensity that varied from 10 000 up to 40 000 shots (arbitrary units) to

I5 generate a protein spectrum (proteogram). The ionized and desorbed proteins were detected and their molecular masses pointed on the proteogram pics were determined using TOF analysis with the Protein-Chip Biology System II software (PBS II; Ciphergen) and the Ciphergen Peaks software. The mass to charge ratio (m/z) of each captured protein by the chip-surface was determined according to externally calibrated standards: human Angiotensin [ (1.2965 kilodaltons, kDa), human ACTH (2.9335 kDa), human 4-endorphin (3.4650 kDa), bovine insulin (5.7336 kDa), and bovine ubiquitin (8.5648 kDa).

Depletion of the protein of ~ 8.6 kDa from EU plasma

Twenty five microliters of magnetic beads (Dynal) washed 3 times with | mL of

PBS were added of 25 pg of anti-A-SAA (SAA-1 & SAA-2) MAb from Clinisciences concentrated at 100 pg/mL and incubated for 18 hr at 4°C in orbital shaking. Anti-A-SAA MAb coated beads were subsequently washed 3 times with | mL of PBS. Five hundred microliters of

EU plasma was then added and incubated at 37°C during 3 hr under shaking. This plasma supernatant was then reanalysed using the appropriated Ciphergen Chip. Five microliters of EU preincubated with anti-A-SAA | & 2 MAD or not were applied and analysed as previously indicated by SELDI-Tof (Ciphergen™).

Inhibition of HIV-1 infecion by recombinant A-SAA protein

Before HIV-i infection iDC cells were incubated for | hr at the designated concentrations with the acute phase human apolipoprotein serum amyloid A (SSA from

Peprotec™) which is an agonist of FPRLI. Subsequently, the cells were infected with HIV-1

ADA or HXB2 at an MOI of 0.1 for 2 hours. The cells were extensively washed and incubated in complete medium. HIV-1 p24 levels were determined by enzyme-linked immunosorbent assays (Beckman-Coulter, France) 4 days after infection.

SAGE Analysis

SAGE was performed essentially as outlined in the detailed of Velculescu’s protocol [7] obtainable at the URL: WW W.sagenet.org with the modifications of Powell [8] and

Kenzelmann [9].

Power Blot Analysis

Immunoblot analysis of proteins was carried out as described (www.translab.com/shtml). Briefly, CD3/CD28-stimulated T cells from the 3 cohorts were lysed by the lysis buffer (Tris 10 mM pH 7.4, Nat orthovanadate 1 mM, SDS 1%), sonicated and clarified by centrifugation. Proteins were migrated in 5-15% gradient SDS-polyacrylamide gels to detect a wide size range of proteins in one gel. Four hundred micrograms of protein was loaded in long well across the entire width of the gel. This translates into near 15 ug of protein clectrophoresed per lane on a standard 25-well gel. Subsequently the gel was transferred to

Immobilon-P membrane (Millipore, Bedford, MA) overnight. After transfer, membranes were blocked for | hr with 5% milk. Subsequently, the membrane was inserted into a Western blotting manifold that isolates 45 channels across the membrane. In each channel, different complex antibody cocktails were added and allowed to hybridize for 1 hr. Following staining, the membranes were washed and hybridised for 30 min with secondary goat anti-mouse horseradish peroxidase (HRP). All antibodies were mouse monoclonal. Membranes were washed and developed with SuperSignal West Pico (Pierce, Santa Clara, CA).

RT-PCR analysis

Total RNA, isolated from activated T cells was converted by reverse transcription into cDNA. For each total RNA sample reverse transcription at 42°C for 50 min, the following reagents were used: | pg total RNA and 200 Units Superscript II reverse transcriptase (RT,

Gibco-BRL); RT buffer as supplied; 100 mmol/L dithiothreitol (DTT), 40 units of Rnasin (Promega, Madison, Wi, USA); 1.25 mmol/L of each dNTP; and 500 ng of oligo dTs. PCR was performed as follow: 2 pL cDNA; 1.25 mmo/L of each dNTP, 2.5 units Taq polymerase (Promega); 2.5 mmol/L MgCI2, 2.5 pL 10X buffer and 20 pmol of each specific primer pair in a 25 pL total volume. The following specific primers were used: IL-22: SEQ ID N°lsense 5’-

TGACAAGTCCAACTTCCAGCAG-3’, SEQ ID N°2 antisense 5’-

TCTGGATATGCAGGTCATCACC-3’; IL-8: SEQ ID N°3 sense 5’-

AACTTCTCCACAACCCTCTG-3’, SEQ ID N°4 antisense 5’-TTGGCAGCCTTCCTGATT-3’;

GAPDH: SEQ ID N°5 sense 5’- CCA-CCC-ATG-GCA-AAT-TCC-ATGGCA-3’ and SEQ ID

N°6 antisense 5’-TCTAGACGGCAGGTCAGGTCCACC-3’. After preincubation (94°C, 5 min), each PCR sample underwent a 29 cycles amplification regimen of denaturation (94°C, 1 min), primer annealing (56°C, | min) and primer extension (72°C, 1 min) with a final extension (72°C, 10 min).

Western blotting analysis

One million of CD3/CD28 activated T cells (as indicated above) from each cohort (HC, EU, and HIV+) were lysed in a 1% NP40 buffer. For each group, equal amounts of protein were electrophoresed under reducing conditions and transferred electrophoretically to nitrocellulose membranes. Membranes were incubated for 30 min in TBS (50 mmol/L NaCl, 20 mmol/L Tris HCI, pH 7.5) containing 5% BSA and 0.1% Tween 20 and then incubated overnight at 4 °C with a primary antibody. Proteins were visualized using the ECL system (Amersham

Pharmacia Biotech, Piscataway, NJ). Blots were washed in TBS containing 0.1 % Tween 20 and incubated with HRPconjugated goat anti-rabbit or anti-mouse secondary antibody (Amersham

Pharmacia Biotech, Piscataway, NJ). For reblotting with another antibody, filters were stripped as previously described [10].

HIV-1 coreceptor phosphorylation assessing

Immature Dendritic cells were stimulated with MIP-14 or with the acute phase A-

SAA (Peprotec™) at the indicated (in Fig 7) concentrations for the indicated periods of time at 37°C. Then the cells were lysed after 20 min on ice with periodic mixing in lysis buffer (1%

Triton X-100, 20 mM Tris HCI pH 8.0, 137 mM NaCl, 15% glycerol, 5 mM EDTA) containing phosphatase inhibitors (I mM phenylsulfonyl fluoride, 5 pg/mL aprotinin, 5 pg/mL leupeptin, mM sodium orthovanadate, | mM EGTA). Cell lysates were precleaned with 30 uL of washed protein A Sepharose beads (15 pL packed beads) at 4°C for 1 hr and 1 pg of polyclonal anti- phosphoserine antibody (BD) was added to 200 pg cell lysates. The reaction mixture was incubated at 4°C overnight. The immune complex was captured by adding 50 uL of washed protein A sepharose beads (25 pL packed beads). The reaction mixture was incubated at 4°C for an additional 2 hours. The beads were spun down (10 sec at 14000 rpm), drained off the supernatant, washed 3 times with ice cold 1 X IP buffer, then were resuspended in 30 uL 2 X

Laemli sample buffer and boiled for 5 min to eluate the immune complex. After electrophoresis on 10% SDS-PAGE precast gel (Invitrogen), the proteins were transferred to nitrocellulose membranes. CCRS was visualized using a polyclonal anti-CCR5 (R & D Systems) and ECL system (Amersham Pharmacia Biotech, Piscataway, NJ).

Human chemokine, Searchlight™ arrays

Four different plasma from each studied cohort were analysed following the instructions the manufacturer of chemokine Searchlight arrays (Pierce Endogen, Perbio, Boston) for the plasma content in 8 chemokines.

Results

Despite being repeatedly exposed to Human Immunodeficiency Type 1 virus (HIV- 1) via sexual or systemic routes certain individuals remain uninfected. To investigate the molecular mechanisms underlying resistance to HIV-1 infection, the inventors have performed a comparative study on CD3/CD28-activated peripheral blood T cells (to enhance cell signalling and gene expression) and plasma (to study their soluble proteins) from cohorts of HIV-1 exposed uninfected individuals (EU), their HIV-1-infected sexual partners and healthy controls (Table 2).

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Complementary genomic, proteomic and cell signalling analyses were carried out using Serial Analysis Gene Expression (SAGE), Surface-Enhanced Laser Desorption lonisation and Time Of Fly Mass Spectrophotometry (SELDI-TOF, Ciphergen™) and Power blotting™, respectively (see Material and 6 Method Section). Understanding of the genetic and physiology of the Long term non progressors (LTNP) and EU individuals with respect to natural anti-viral mechanisms could provide the basis of the treatment against HIV infection. The inventors have then studied physiopathological mechanisms on the basis of the absence of infection in individuals subject to frequent exposures to HIV in EU individuals.

First results obtained from the high number of gene tags (HC: 21193 tags, EU: 22697 tags, and HIV+: 17 285 tags) of transcriptome analyses by the SAGE method exhibited that in EU were found to overexpress the Th1 IL-22 and SOCS1 and that Granzyme B was to underexpress in HIV+ compared to EU and HC cohorts that exhibited similar levels (Table 3) these results of course were obtained without having any “a priori” idea.

SAGE

Gene level expression (ES EN NI I

RT A EE

Power blot

Protein level expression

ELLA I NCI NU in parallel using Power Blot analysis of proteins from pooled T cells from the 3 cohorts the acute-phase response factor STAT3 was detected. The plasma analyses (using SELDI-TOF approach) from 25 individuals per cohort have shown an expression increase of a soluble protein of a MW of ~8.6 kDa, (Fig. 2).

Taking into account that TL-22 initiates a cascade (Fig. 3) of innate immune response [25] that includes the Jack/STAT pathway, SOCS 3, beta-defensins, and the acute phase apolipoprotein serum amyloid A (A-SAA) : SAA-1 and SAA2 , these data were further developed using different methods to confirm and extend their signification (see Material and

Method Section). Synthesised in the liver and in other tissues as epitheliums of blood vessels, the

ASAA is found associated to HDL [26] and HDL-free in the plasma. The A-SAA promoter is highly responsive to inflammatory cytokines such as IL18, TNF4, IFN& and IL6 that can be induced by LPS. Moreover recently, it has been shown that the Th IL-22 cytokine is able to participate to A-SAA expression. These observations have suggested that A-SAA could play a role as an immune innate defense molecule at local sites [27]. Post transductional cleavage of A-

SAA produces C-term fragments of approximately 8.5 kDa MW [28, 29]. To identify the ~8.6 kDa protein obtained from the SELDI-TOF analysis, a specific anti-A-SAA MAb before the plasma SELDI-TOF profiling was used and as shown in Fig. 4 the pic corresponding to ~8.6 kDa

I5 was depleted using this anti-A-SAA MAb. Interestingly, it has been also known that A-SAA is able to induce the IL-8 cytokine [30] then an IL-8 specific RT-PCR was performed from 5 individual of each cohort to verify that this cytokine characterize the EU cascade. Figure 3 clearly shows that the PCR evidence a specific polymorphism of IL-8 in EU in comparison with the 2 other groups (HIV+ and HC).A specific IL-22 RT —PCR was also performed (Fig. 6) in each individual that formed the pools and we could observe that only EU overexpress significantly this important Thl cytokine.

Other controls and validations were done, thus Western Blot analyses were done on proteins from pooled samples. It was also observed in EU group that STATI and STAT3 were phosphorylated (Fig. 7A and 7B), whereas STATS was down regulated in HIV+ but higher and equal level of activation in both HC and EU groups (Fig. 7C). The expression of SOCS3 protein (Fig. 7D), a STAT3 responsive gene, was upregulated in EU. Furthermore, these EU individuals were shown over-express alpha-defensins [15]. Moreover, it has been shown that IL-8 is able to desensitize HIV coreceptors through FPR receptors family [31, 32] and that Statl is necessary for cell antiviral factor (CAF)-mediated inhibition of HIV-1 Long terminal repeat (LTR) activation and HIV replication [33].

Since agonists of FPR and FPRL1, soluble A-SAA, the WKYMWYVm peptide, the bacterial chemotactic peptide fMLF, and probably its ~8.6 kDa fragment), induce phosphorylation as shown in our experiments using A-SAA in specific Western Blotings (Fig. 8) and downmodulation of both the HIV-1 coreceptor CCRS5 and CXCR4 through FPR activation 5S [34-37]. Then as reported [31, 37, 38], it has been shown that A-SAA protein inhibited HIV-1 infection (Fig. 9).

The A-SAA purchased from Peprotec™ used in these assays exhibit the ~8.6 kDa fragment (Fig. 10)

These results allowed to identify a cascade of events that favour the innate host resistance to HIV infection characterizing EU. Since IL-22 is able via JAK/STAT to induce the

Beta defensins, A-SAA and that A-SAA induces IL8 secretion [30] of its expression, these results clearly depicted this cascade. Moreover, IL-8 [31] and a-Defensin [39] have been shown to decrease HIV-1 infection. Altogether our results show that 1L-22 is a starter cytokine helping the innate immune response that provides resistant mechanisms to HIV infection (Fig.2).

An other exploratory approach was to check some chemokines in plasma from 4 individuals per cohort (EU,

HC, HIV+) by using the Serchlight (Perbio ™) human chemokine array (Table 4).

Eight chemokines from Search light array (Perbio) [P10 | TAC | Mif3a | MIPSb | GRO A ] Exodus-2 | Lympho | SOFIb |]

Sample [ Pyml | Pym | Pgml | Pyml | Pyml | Pgml | Pgmi | Pgml hci | 30a | 404 | s2 | 173 | 83 | 86 | 246 | >625

Hc2 | 190 | 10i0 [viz [703 | 302 1 97 | 525 | 434

Acs | 00 | aig | 62 [ 372 | 160 [| 81 | 169 | >625 nhc4_; 93 | 24 | ug | 431 | 358 | 101 | 706 | 698

Eul | 306 | 526 | 98 | 67 | 614 [| 79 | 606 | S508 —EU2 | 906 | 1053 | 139 | 855 [ 193 [ 10 [ 671 | S41 __Eus | 616 | 556 | 155 | >200 [ >200 | 218 | >800 | >1600

Eva | 253 | 814 | ter | 872 J 21s J 10 |] 186 | 351

THW+1 | 30 | 432 | 73 | 120 | 173 | 66 | 41 |] 342

Av+2 | 687 | s7a | 68 | 483 | 123 T 109 | 345 | 329 ves [28 | ea | 83 | ase | 127 | Ba | 40 | 460

TRV+4d | ent | 868 | 7s | 865 | 60 | 88 | 397 | 343

GRO-0, MIP-3B, SDFI-f} and the gamma chemokine lymphotactin were found to be highly overexpressed in some EU and sometimes in HC, compared to HIV+. The role of these chemokines in HIV infection is not clearly elucidated but Lymphotactin show an anti-HIV activity [1]. However, it is possible to consider the existence of a specific polymorphism of these chemokines that could have an anti-viral effect (individually or combined) of some EU taking into account that in our EU studied cohort we have found an IL-8 polymorphism specific of EU.

Additionally the SAGE analysis interestingly shows that Granzyme B was down regulated in

HIV+ but maintained in EU and HC individuals, This confirm the observation of the loss of granzyme made in HIV-HAART treated individuals [2, 3]. The inventors have also observed in

SAGE analysis that a higher production of IFN-gamma in EU than in HC and HIV+. These cytokine is typically antiviral which has been found in some studies on EU made by others.

TABLE 4

Eight chemokines from Search light array (Perbio) [P10 | TAC | MiP3a | MIP3b | GROA | Exodus-2] Lympho | SDFIb |]

Sumple | Pym | Pg/ml_| Pym | Pym | Pym | Peml [| Pym | Pg/ml a04 | 52 | "173 | 87 | 86 | 246 | >625 101.0 _HC3 1 200 | 419 | 62 | 372 | 160 [ ®&1 1 169 | >625 _HCa | "993 | wi24 | 118 | 431 | 358 | 101 | 706 [| 698

EUT | 306 1 sa6 [98 | 617 | 674 | 79 | 606 | S08

EU2 | 906 [| t0s5 [| 139 | 8&5 [ 1193 [| 11.0 | 671 [ S41 _Eu3 | 616 | ss6 | 155 | >200 | >x00 | 218 [ >800 [ >1600 eg4 | 53 | kia 1 vor | 872 | 25 } 110 | 186 | 350

Hive 331 432 | 93 J] wo | 13 | 66 | 41 | 342

HIV +2 a YY, i 83 | 459 | 17 1 84 | 490 | 460 _Aiv+a | ari. | 868 | 75 | 85 | 660 | 88 [| 592 [ 343

Taking into account that the cascade of events was found to induce several and major elements of the innate immunity, the scope of the invention also extends to other viruses and retroviruses than

HIV. it will also be considered that the EU exhibited higher amounts of phosphorylated STATI and that importantly this element is essential to the activity of the “cell anti-viral Factors” (CAF) secreted by CD8 T cells. It has also been shown that HIV+ appears to loose the Granzymes B in comparison with EU and HC. Granzymes B is produced by CD8 T cells and NK to kill infected cells. The STAT-1 dependent production of CAF Granzymes B plays major role in the anti-HIV activity in persons that resist to AIDS development despite their HIV infection.

It has also been observed in SAGE analysis that a higher production of IFN-gamma in EU than in

HC and HIV+. These cytokine is typically antiviral.

These cascades elements should be involved not only as element of the resistance to the viral infection but also as element of the resistance to the induced disease.

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Claims (20)

’ PCT/EP2004/013393 CLAIMS

1. The use of IL-22 is as a biomarker of the resistance to viral infection when measured as gene expression or as level of cytokine.

2. The use according to claim 1, wherein IL-22 is used in combination with a soluble protein of about 8.6 kDa as identified in plasmas by SELDI-

TOF.

3. The use according to claim 1 or 2, wherein the viral infection is an HIV infection.

4, Use of IL-22 as starter cytokine in the manufacture of a preparation for favouring the innate host resistance to viral infections, by helping the 16 innate immune response to infections used as prophylactic agents in triggering the innate immune response to viral infections.

5. Use of IL-22 as starter cytokine in the manufacture of a preparation for favouring the innate host resistance to viral infections, by helping the innate immune response to infections used as therapeutic agents in triggering the innate immune response to viral infections.

6. Use of claim 4 or 5, wherein IL-22 is used in combination with a soluble protein of about 8.6 kDa as identified in plasmas by SELDI-TOF.

7. Use according to claim 3, 4 or 5, wherein the viral infection is an HIV infection.

8. The use of IL-22 as an adjuvant and an innate system inducer in prophylactic or therapeutic compositions for viral infections.

9. The use according to claim 8, wherein the viral infection is an HIV infection. AMENDED SHEET

: PCT/EP2004/013393

10. Pharmaceutical compositions, comprising an effective amount of IL-22 in a form of cytokine or encoding DNA in association with a pharmaceutically inert vehicle.

11. The pharmaceutical compositions of claim 10, for administration by the oral or mucosal route or by injection.

12. The pharmaceutical compositions of claim 11, wherein for oral administration, the pharmaceutical compositions are presented in the form of tablets, pills, capsules, drops, patch or spray.

13. The pharmaceutical compositions of claim 11, wherein for administration by injection, the pharmaceutical compositions are under the form of solution for injection by the intravenous, subcutaneous, or intramuscular route produced from sterile or sterilisable solution, or suspension or emulsion.

14. The pharmaceutical compositions of claim 11, wherein for mucosal administration, the pharmaceutical compositions are under the form of gels.

15. The pharmaceutical compositions according to any one of claims 10 to 14 for preventing or treating viral or retro-viral infections, particularly HIV-infections.

16. A multifactorial innate immunity assessment method, comprising the use of IL-22 in research diagnostic products.

17. The method of claim 16, further comprising the use of a soluble protein of about 8.6 kDa as identified in plasmas by SELDI-TOF. AMENDED SHEET

) PCT/EP2004/013393

18. Use according to any one of claims 1 to 9, substantially as herein described with reference to and as illustrated in any of the examples and accompanying sequence listings.

19. A composition according to any one of claims 10 to 15, substantially as herein described with reference to and as illustrated in any of the examples and accompanying sequence listings.

20. A method according to claim 16 or claim 17, substantially as herein described with reference to and as illustrated in any of the examples and accompanying sequence listings. AMENDED SHEET